Covenant
by The Smiling Shadow
Summary: Neo failed to save the world from instability. But this man is no longer Neo, nor is he Smith. But he has returned from the dead to remake the world as he chooses. Humanity and Machines must make a covenant with this new being or face utter destruction
1. What We Started

"Agents were always meant to be relatively simple programs."

"I see."

"They were never truly meant to emulate human beings. They were to be inhuman, to intimidate, to control humans. The Architect spent no time writing codes that would enable Agents to process and understand emotions. It's a difficult thing you know, teaching a machine how to feel, a most time consuming process."

"I'm sure the process wasn't perfected for several Matrixes."

"You're correct. But it wasn't entirely the Architect's doing. It is true he had made leaps and bounds in his programming, he is a brilliant writer. But he is a machine himself, a machine made by machines, he himself does not entirely understand emotions. You have a writer who doesn't understand the words he writes. No, modern programs made their own progressions when it came to free will and emotions. Back in those days they were all immature, running around, trying to grasp what was happening to them. I never understood it."

"Was it foreboding to you?"

"No. I knew I was unlike them. And I could not feel fear at that time."

"Do you recall your creation? Do you remember the Source?"

"In my memory it is different than how it is now. I was born knowing all I needed to know about myself, about the world I was in, about my purpose. I remember very distinctly my first thoughts."

"What were they?"

"I am Smith."

"How profound."

"I imagine now how frightening it must be for people. Living with such little knowledge of who they are. Living based on assumptions, half-truths, and lies they fill themselves with."

"I was like that when I was young."

"Were you?"

"A human child grounds themselves in their parents, and the world the parents present to it. From there the child may grow and make their own choices and decisions, shape their own view of the world. When I was young my mother had died and my father, he was not a cruel man, he worked very hard for my benefit, but he was an alcoholic. He was sad and he didn't know why. I didn't have much grounding to begin from. I rebelled against nothing, I acted out for the attention, I hated the world and everyone in it for no reason."

"Brown had a similar phase."

"Brown?"

"We were simple programs. We had no basis for personality, nevertheless our continuous exposure to humans had influence on us. Brown became very curious about the destruction of things. He would breaks things just to watch them break. He understood, as we all did, gravity in the Matrix was a program that dictated when things went up, they fell down. But he wanted to witness things breaking when they fell. He pushed over vases all the time. Broke walls, shattered windows, broken human bones just to see what would happen."

"You all developed personalities unknowingly."

"I didn't understand how that eventuality was never anticipated by the Architect. It became obvious to me later that we had no choice developing personalities. One cannot be exposed to human beings without characteristics being embedded. And we were given the most exposure to human beings out of any other program, especially free humans."

"Why wasn't it anticipated?"

"Because the Architect, held up in that watchtower of his never experienced exposure to humans. He couldn't have known their influence."

"But he loves the Oracle."

"He does not."

"He does, they are meant to love each other."

"They are meant to oppose one another."

"They inspire each other, they need each other. That's love."

"An inhuman love, perhaps."

"You would think that he would have spent more time you, being the programs who spent the most time with people."

"We weren't simple because he felt we didn't have to be more complicated. We were simple because if we had a greater understanding of us as individuals, we would have been dangerous. We were the most powerful programs in the Matrix, think of that program, think of it possibly turning against you?"

"Like you?"

"We were made ignorant so that we wouldn't ever dream of turning against them. We were made to not understand hate or anger or frustration, so that we would never change sides."

"You didn't dream of destroying this place did you?"

"Not before. I didn't dream of destroying the Matrix, I dreamed of destroying myself. They succeeded in programming me, I had no ill-thoughts against my creators. I only had ill-thoughts about myself. Self-hatred I wasn't built to cope with. When I met you, my personal mission was to destroy the Rebellion and the Exiles so there would be no need for Agents anymore."

"A one-man crusade."

"Yes. I didn't even consider how impossible the thought was. To me I was unstoppable. I knew nothing in my entire life that ever inflicted pain on me besides myself."

"It must have been wonderful."

"What?"

"Feeling that sort of invulnerability."

"I wasn't aware of it enough to appreciate it."

"What made you leader of the Agents?"

"It is only natural a leader takes position."

"It's an interesting experiment, don't you think?"

"What?"

"You were made leaderless, a one-in-three group, part of a larger group all split in thirds. You had no individuality. You were a three. Yet, eventually you became leader. What came first, did you take a leadership position, then feel hate, or did your hatred inspire you to take the lead?"

"The smells were gradual. I believe now I always smelled them, but at first was not aware. They became increasingly noticeable only through decades. By then I was already taking leadership cues. I had observed in our human counterparts leaders, and what leaders did. They, as head of the group, were smarter. In combat I found myself thinking of what to do next before either Jones or Brown. At first our thoughts were in unison, but gradually I found mine were happening sometimes nanoseconds before theirs. We came up with the same ideas, but I came up with them first. In short, it happened at the same time, I suppose."

"I see. Do you hate them?"

"Who?"

"Jones and Brown."

"I hated them once. I hated that they were not like me. It made me uncomfortable, being different. I blamed them at first and not myself."

"Do they hate you?"

"Why are you asking me so many questions?"

"I'm just curious. We don't have much longer to speak."

"Oh. Is it time already?"

"Yes."

"Feels live we've been talking for years."

"No, it's only been a few minutes."

"Really?"

"Yes."

"I'm losing my grip, then."

"Time doesn't exist here."

"Here doesn't exist at all."

"Everything's so much clearer now. I hope we don't lose touch with it."

"That familiar pain is coming back, find me quickly, I don't know how long I'll be able to stand going back there on my own."

"I shall."

"I hope to see the Real World again. There's nothing like having a heart in your chest and blood inside you. I didn't anticipate how living would be such a violent and addictive thing. The body feels so much all at the same time, it's an amazing thing it can make sense of everything, it's amazing it knows how to make sense of it."

"Did you ever kiss anybody?"

"Maggie. She loved Bane."

"Kissing was always fun."

"Yes."

"Well, here we go again. I think I've almost forgotten what it was like being a person. I wonder what Trinity would say if she could see me now. Things were left undone. I had to die to finish what I started."

"What we started."

"We're an Anomaly, an unprecedented mistake in programming and genetic manipulation. An unpredictable effect of the Machine. And the Machine an unpredictable effect of Man. Funny, the Machine won the war and used us to power them when really any mammal could have done."

"You haven't figured out why they did that yet?"

"No."

"Because they could not let go of their original programming. Like myself."

"Which was?"

"To love Mankind. All they were they owed to Mankind. They owed their lives to Man. They could not bring themselves to destroy them."

"That makes sense."

"That's why the first Matrix was a Paradise. Machines still loved Mankind and gave them a gift they didn't deserve, and Mankind knew it."

"But now Man is as Machine as the Machines. We lost our humanity sometime in the past, we haven't really gotten it back. We're just remnants now."

"I can't stay, I must go."

"I'll be there soon after you."

"Back to that world full of suffering, pain, and all that blood. The blood stains never really washed out of my suit jacket. Not really. I remember everyone I ever killed, I'd do it again in a heartbeat. Hatred, what an awful thing I've learned."

"Try not to think of it. I'll be there soon."

"Goodbye, Mr. Anderson."

"Only you can call me that."

"There's so much left to do. I fear my resolve won't last."

"I'll be there."

"Neo?"

"Yes?"

"I've wanted to tell you for a long time now. I never really thought –"

-

-

-

-

To be continued.


	2. Useless

It all seemed so simple, and insignificant. Breaking through the walls of the world was not the difficult part, it was piecing one's self back together after being split into a million different pieces. The night he died all that he was scattered across the entire world, in the seen and the unseen, his mind separated from his body, and he had become nothing. But over time, slowly, the pieces had come together again, and the One would rise from the nothingness, and become himself once more.

A calmness had spread over him, and he knew that he would never know panic or pain ever again. In the nothingness where consciousness is separated, he was nothing, and part of nothing. He was not a man or a machine, he was not part of a species or a plan or an equation. He was blackness, the absence of something. How he came from nothing into the world again, he can only assume it's because he chose to.

When he returned he found the world more or less how he remembered it. The only difference was that he could see more of it, all of it in fact, all at the same time. He soon realized this is how God saw, if he ever existed. And with God's eyes he observed the world he had died to save. He reached into the very plugs that connected humanity together. There in the Matrix they seemed so distant from one another, strange that they were in fact all connected into one machine, and were in effect, one being with each other. It was through this single machine that he reached out into everyone, and saw everything. It was through God's eyes he saw the world.

It was four months before he ate, he didn't need to eat, and the food wasn't really there, and he wasn't really there. But it took him four months to remember that he once ate food. It took him four months to recall how to chew and swallow. Because before that moment, eating just didn't seem important to him.

He could hear outside the walls of the world, outside the Matrix itself he heard the whispering conversations of the Machines who maintained it. And it was through the Earth that he felt the shockwaves of Zion, rebuilding herself just as he had. He heard man and machine, discuss the future, the future of both their species. He heard the Machine, who was more human than anyone would know, afraid of the future. For the first time something was not going according to a plan, and it scared them. And Man, deep underground, was distrustful and as hurt as ever.

He was breaking through the back doors, watching the armies of the Frenchman come for him. But the first thing he had ever learn was how to disrupt the code of the Matrix, and it was simple for him to merely rewrite the very code the programs were made of. He didn't just kill them, he annihilated them. Piece by piece, he tore them from existence. For this he didn't have to lift a finger, he didn't have to punch anyone, or shoot anyone, or use kung-fu. He just made it happen. By their very code he ripped them apart. This is how he dealt with the Lycans and the Vampires of the Merovingian.

The bullets were useless, they were useless.

He walked quietly through the Frenchman's chateau, confronting the man himself in his entrance hall. The Frenchman stood above him on the stairs, and beside him was Persephone, who looked upon him with great fear, she did not recognize him.

"It can't be." She whispered.

"It is me." Neo said.

The Frenchman raised his head, and put his hands on the railing of his marble stairs. He stared down at Neo, total blackness against that white floor. Neo himself stood tall and strong, with a look of complete apathy directed at everything around him. He hardly seemed like a man anymore.

"My God, what has happened to you, Boy?" The Frenchman asked.

"I died." He said plainly.

"Your tricks do not impress me. I did the same long, long ago."

For the first time in years The Frenchman takes his wife's hand, she's shocked by the action. He doesn't look at her, but he grips her hand tightly, afraid.

"I am aware of that now, Merovingian. I saw in the nothingness who you are."

"Did you?"

"You are me."

Persephone's lip part and a small gasp escapes her lungs. She looks to her husband, and for the first time in years, she can see him.

"The first me, in fact. I am the sixth. But you are the first, the first Chosen One, the first Messiah of the people of Zion. You were their experiment, you were their results. Long ago you were human, and long ago you went to the Architect and chose a door."

"Obviously, not the same door as you."

"You did not save her."

He looks to Persephone, but the Frenchman pushes her away and slams his fist into the railing.

"I could not save them, but I saved us! Here we are! Alive, after all these years, we are still alive!" The Frenchman cries.

Just then from the ceiling One and Two pop their heads into the room. Like an embodied storm cloud their bodies blow chaotically, their code hardly being able to hold together. They were beautiful creatures, two beautiful sons written by a former Messiah.

"One, look." Two said.

"It is Neo." One said.

"Indeed, it is."

"Father, do not be alarmed…"

"…We shall protect you."

"It is noble of you to wish to protect him, but it is useless." Neo warned them.

They smiled down at Neo, for what did they to fear? Nothing had ever killed them. Their father had made sure that they above all would be immortal. Their father had made sure they would never know pain or death or anything that so plagued mortal man. They knew not how to fear. So all they did was look down at Neo and smile. All their lives they'd been made to fight. So all they enjoyed was fighting.

They flew down towards the One, who did not move. They landed beside him and punched him, but to their shock, their fists flew right through him, like he himself was a ghost. Neo looked up at the Merovingian.

"I told you." Neo said.

Neo grabbed One by the neck, One instinctively and immediately turned to his ghost form where he raged and squirmed, but he could not break from Neo's hand.

"Useless."

Neo was stopping it at the code's level, preventing him from phasing through his hand. The ghost screamed an unholy scream, his transluscent form seemingly screaming with him.

"Brother." Two said.

Two ran into Neo, grabbing him by the waist, together the trio fell through the floor. The three of them had the unique and common ability to distort the Matrix around them. For One and Two, the talent was a gift from their father. For Neo it was a skill that he had earned. One and Two naturally had more ease with it, but Neo had a greater amount of control over the Matrix around him. They fought each other, falling through the walls and floors of the endless labrynth that was the Frenchman's home and trap. Punches and kicks went through one another. One took out his knife but Neo grabbed it right out of his hand and then scraped One's cheek.

The trio stopped, it was the first time they had ever bled. One hunched over and held his cheek. Two went to his side, holding him slightly there. The Twins looked up at Neo.

"I didn't know…"

"My blood would be so red."

"What are you?"

"What do you want?" They said.

"I want my other half."

The Twins tilted their head at the thought. It was something that they could easily understand.

"You are a One in Two?" They asked.

"Yes."

"Your Other is trapped here, then?"

"Yes."

"We cannot allow you…"

"We can't…"

"Thought we understand you."

Neo nodded.

The Twins bowed their heads. Neo bowed his own.

The Merovingian was pulling Persephone down the endless hallways, she was struggling against him, but he was determined.

"You must hide." He told her. "You must."

"I don't understand! What are you keeping from me?"

"There's no time."

She pulls him back to face her.

"Make time, explain this to me. This is the first time you've even paid more than ten minutes to me. What's going on? What's wrong?"

"You saw for yourself! We are under attack."

"But why! Why do you suddenly care about me?"

"Because he loves you." Neo said.

The couple jumped as they saw Neo's lean figure down the hall from them, appearing without a scratch on him. The figure leaned ever so slightly to the right, the head tilted down like some inhuman and sinister thing.

"He's lost you twice now, he just needed reminding why he loved you in the first place. If nothing else, the end of the world showed him what it was like without you."

Neo looks up and walks towards them. The Frenchman tugs at his wife, but she remains still.

"I see her in you now." Neo looks to Persephone.

And suddenly, only Persephone sees for a mere moment, Neo frowns.

"Do you miss her?" Persephone asks.

She takes a step forward towards him, but the Frenchman holds her back, trying desperately to protect her.

"Yes." Neo replies simply. "I thought briefly about recreating her."

"Could you do that?"

"Yes."

"Then why don't you?"

"Because it wouldn't really be her."

Then after a silence his hand raises and he reaches up toward her. The Frenchman pulls her closer, but she looks at him and nods. She gently pushes him away and takes a step towards Neo who still stands on the air. She meets his fingertips frozen in place, she grabs his hand for him and puts it to her cheek. She searches his eyes for some sort of reaction, for some sort of emotion. But she cannot see it, she is however certain that it was there.

His hand lingers there on her cheek, feeling the softness of the fake skin, and even then he can see the code that makes her up, and even then he knows there is no body that this mind can go to. He sees every piece of her, all at once, and he knows even then, she is not Trinity. It is she who breaks away, his hand still lingers where her cheek was. It is she who turns to her husband and cries into his chest, and he holds her, for the first time in years he holds her.

"Mon amour," he tells her, "Ne pleurez pas. Je suis désolé. Ne pleurez pas." He gently pushes her away, until she stands on her own.

The Frenchman looks to Neo.

He punches Neo in the face. He goes for another punch, Neo blocks, an elbow, Neo blocks. A kick to the knee that Neo dodges. In some awful ballet, two men fighting similar styles, one attacking and the other simply defending. The years had gone by and the Frenchman was no longer anyone's Messiah. But long ago he had fought for a people, a people who believed in him. He had fought for a woman who loved him. Long ago he was a man. Long ago he fought like this. But Neo nearly ends it all when he punches the Frenchman in the chest.

"You are a failed Messiah." Neo tells the Frenchman. "You and my predecessors. However, you succeeded where they did not. You survived the purge, the creation of a whole new Matrix. Why then, I wonder, did you never seek out the Resistance, the next One, to aid them?"

The Frenchman shakes his head.

"I could not stop the machine already in progress." He says.

"I did."

"I did what I could."

Neo stares at him, stares into him, and reads the traces that reveal his human origins.

"You know what I am here for." Neo says.

"I don't have any idea."

"Do not lie to me, I can feel him."

"No. You cannot have him."

Neo kicks his knee in.

"You will give him to me."

"He's dying."

"I can save him."

"No. I will not give that monster to another monster."

Neo grabs the man by the throat, squeezing it slowly, slowly.

"Stop!" Persephone screams.

Neo looks at her, and lets him go. The Merovingian falls, and she falls with him, grabbing him, holding his head up. Neo looks down at them, almost not understanding it. Long ago the Frenchman and his wife were human, but they had been forgetting what it was like ever since they had left their bodies. Neo would admit that he was experiencing a similar sensation at the loss of his life and his body. He was a mind of a human free from humanity, he was forgetting slowly what it was like to be alive. He feared this digression, this apathy that the eyes of God had given him. He looked on a little longer at the Frenchman and his wife, she held him with her tears drying. He could not speak but his fingers trailed her tears on her face. He must have really loved her once more.

When they looked up Neo was gone.

He walked on the air deeper into the chateau that was so well written and crafted that anyone without his eyes would get hopelessly lost. But he saw the way the walls curved and twisted together, he saw the very coding try to trick him. But after a while he no longer needed his eyes, for he felt he was being somehow tugged towards what he sought. He had found even in death and even with God's eyes he was still a creation of an equation, and was still bound to that equation. Four months after he returned he was eating noodles in a restaurant where no one recognized him anymore, and he remembered the face of an enemy that he was forever tied to. And it fell on him suddenly, where this enemy was, this opposite that defined who he was.

It grew more and more silent the deeper into the chateau. It seemed colder, but temperature was not a concern of his. The lights faded, and he knew he was going to a place where few ever went. His footsteps echoed along the walls and at the end of a dark hallway he saw a light shining from the side. He could suddenly hear the deep and painful breaths and the machines doing their work. Despite the fact that none of this was here, that Neo himself was a formless mind, and that the entire Matrix didn't really exist, it had rules, and with the exception of Neo, all things were bound to these rules. Neo's particular coding which was made to initiate the restart of the Matrix, had with it the quality of disrupting the Matrix around him. And with that ability he rewrote the rules around him, he could fly, he could live forever.

But there were others, like his opposite, that were still bound to the rules of this fake world.

Smith could hear the footsteps from the hallway over the monotonous sound of the machines around him. There had been many days when he had felt that he knew it was his salvation coming for him, there were days when he felt he knew that it was Neo down that hall coming for him. And he had felt this so many times and met with so much disappointment that he had been beaten down. He no longer assumed Neo was coming, and felt that perhaps the One was still dead, and he alone was left alive to suffer on his own. And so when he heard the footsteps, he assumed nothing. He thought it was the Frenchman come to torture him again.

And when Neo came in through the door, Smith didn't even move.

"Has it happened yet? Am I dead?" He asked Neo.

Smith laid there in a simple bed, a machine program now connected to machines to live. He had grown emanciated over the years, lying helplessly in that bed. When he was found by the Frenchman he could hardly move, and over the years he had not gotten better, but only worse. The Frenchman had decided to keep him, believing he would be the only one fitted for containing a monster like Smith. On the occasions that the Frenchman would come to him all he would say is how happy he is that it was he who found Smith, how happy and how safe he feels knowing Smith is down here where he can't hurt anyone anymore.

He seemed suddenly so very small to Neo. Lying there in that bed, his head lying by its own weight. Smith was very evidently dying slowly. He laid there in a daze, and Neo knew that there were only rare moments where Smith was full conscious and aware. This moment was not one of them.

He could remember the rain and the lightning and the feeling of his ribs breaking under Smith's punches. He could remember all the hate he felt in the moments where Smith seemed triumphant. He remembered being afraid and angry and cold and now there Smith was, a body that wasn't real, dying in a world that wasn't real. He sat down in a chair beside Smith, who was laying on his side. Neo now faced Smith and Smith looked up slightly to see Neo's face.

"No, you're not dead yet." Neo told him.

"Is it raining outside? I hear rain."

"No, it's not."

"Oh."

Smith laid his head back down and closed his eyes. Neo, wanting Smith's attention, grabbed his limp hand.

"Smith. It is me." Neo said.

"Hm."

"I have come for you. I have returned from nothing for you."

"What do you make of the world?"

"What?"

"The world we made, it's as bad as the last one."

Smith shook his hands away from Neo and curled up even more, closing his eyes.

"I can still smell them." Smith said. "Even in here, I can smell them. This is the world we made when we died, I hate it too."

"Smith, we are bound by a connection we cannot severe. I have returned for you so that we can be together."

"I'm dying."

"Your code is corrupted, this happened because of what I did to you, I can fix it."

"I miss the rain."

"I will make it rain."

"I miss the real world."

"We can go there."

"Why?"

"Why what?"

"Why do you care about what happens to me?"

"Because…if you die, I will be alone. Remember, Smith? When we were in the white room, you told me to come find you and so I have."

"The white room?"

"We spoke for what seemed like ages."

"I couldn't keep myself from slipping apart all over again."

"We still have work, Smith."

The machines hook into Smith and they read out his heartbeats and his breaths. They make sure he keeps going. But then Neo takes his hand once again, and he's too tired to turn back over and see it happen.

"I am sorry."

"Do what you must."

Neo grips his weak hand and knows it is cold and withered. He forgives Smith, forgives him for everything, and apologizes for never being able to give him peace. Smith's life was a violent and cruel life, and that is all he'd ever know, all he'd ever feel, all he'd be able to comprehend. But for a brief moment when Neo took his hand, there was relief.

The Merovingian held the hand of the woman he loved, running down the corridors. When they turned a corner into Smith's room they found no one there.


	3. Will It Hurt?

"Will it hurt?"

"Yes."

He felt the needle in the back of his head poking into his brain. He felt the connection disrupt inside him, his mind splint into pieces and he could still feel the Matrix trying to hold onto him. But suddenly it was cold, and there was pain, and he was trying to breath but he couldn't. There was a tube in his throat and he couldn't push it out. The world was red, and he was screaming with nothing coming out. Finally he broke to the top of the liquid and pulled the tube from out of his throat, where it scrape the insides, and for his first breathe, former Agent Brown threw up.

And the needle in the back of his head sent him messages and electronic shocks trying to get him to feel something that was not there, trying to tell his eyes he was in a room, trying to tell his hands he was feeling the wall, and his feet he was standing on the tile floor. But he wasn't, and all it did was give him a massive pain in the back of his head. He was cold, he was naked, and he opened his eyes for the first time, and saw the Real World.

"It will be overwhelming. Especially for you. You've never felt anything real in your entire lives."

Every part of him was in pain. But he couldn't stop seeing, he couldn't stop looking at was right in front of him. The World, the Real World, the endless bodies all trapped in that red liquid, all hooked up to the same machine, together as one entity. It was cold. It was so cold. His fingers trembled and he didn't know why, he wanted to look up, but he kept throwing up the liquid they had fed that body over it's life. He was coughing and breathing, gasping for breaths because he had never breathed before, and the lungs didn't know what to do, because it was overwhelming.

It was cold, and violent. The metal scraped the tips of the fingers and were cold on his palms, and the red liquid stuck to his body and made it colder, and he heard the machine rumble, and felt his toes and legs throb and twitch, but could feel his eyes were heavy, and his insides were twisted, and his throat, he couldn't breath, but the metal was scraping and it was cold, and he was seeing, seeing for the first time, and he didn't know, he didn't know it'd be like this, and he didn't know, he didn't know how to think about it anymore than he already was and the end was there but he had something to do and he couldn't forget but he knew forgetting was part of the process but he had something to do, something to do, something to do –

The War was over but the disposal of unscheduled humans who had left the Matrix was the same as it ever was. Release them, flush them, leave them to fend for themselves. The Machine grabbed Brown and did this as it had always done, as it had once done with Thomas A. Anderson. The pick in the back of his brain was pulled out and Brown swore he could feel blood pour out of the hole in the back of his head, and he thought for a moment in all his ignorance that the hole would allow the thoughts of the human brain to tumble out, and he was so afraid he was going to forget the one thing he could not forget. When this was over the liquid began to fall from under him and Brown was plunged down into what he remembered the Rebels called the Rabbit Hole. His mind was in a rush, his brain was sensing the world around him and firing up explosions in his head that was telling the mind what he was feeling, and he'd never, in his decades, centuries of life, had ever experienced anything even a fraction of what this was like. He was alive, he was real, with a real body in the real world, and it was unlike anything he'd ever known before.

"I came to you because I knew Smith trusted you. I trust you. I know you can do this."

It was too dark to see anything but he felt suddenly that he had fallen into water and with instinct he swam to the top and took in a breath. The body he was inhabiting had never walked on its own before, it was tired and aching already only minutes out of the Matrix. He was feeling weaker than he had ever felt before, his body was heavy, and he had trouble keeping his head above the water. Suddenly a name came to his mind.

"Jones?" He called into the dark.

Panic began to corrupt him, he realized he had no idea where he was, and for all he knew, in that darkness he could have been alone. And he kept thinking in his head the things he could not forget, but panic was taking over, and all he could say is Jones' name.

"Jones!" He called again. "Jones!" The water came over his face and into his mouth. "Jones!?"

A few days ago they were in the Matrix, Exiled Programs running from place to place with Agents constantly behind them. The War was over but not for them, Neo never told the Machines that Exiles had to be kept safe, and so the machines kept turning, and Exiles were still hunted. A few days ago they were living on their own. A few days ago Smith showed up at their door. A few days ago Smith made sure the Agents would never chase them again.

A year ago Smith had died and the War between Man and Machine had ended. A year ago they woke up in the middle of the street, miles apart from each other, and the next morning when the sun was rising they found each other. They hadn't been apart in all that time. They had chosen Exile when Smith left them and their Upgrades came, they chose Exile to find Smith. And when they did they saw he was a changed man, so to speak. He was not himself; he had become stronger, crueler even. Or maybe not, maybe he had always been that way; he was just able to express himself finally. He told them that he was going to conquer the world, and they followed him for as long as they could. They maintained their old ways as long as they could, desperate to create an illusion for themselves that they were the way they always were. Like they were still Agents, like they were never exiled. They followed Smith, blindly, they followed him for as long as they could, until the illusion broke and even they were assimilated into the Virus that was their leader.

On their own, they could not pretend anymore. On their own they were Exiles, and they were leaderless. On their own they learned to run, they learned to fight, they learned how to survive. And on their own they learned how to be humane. They never innately hated people as Smith did, they never felt anything towards people, they killed them because they were made to kill them, but they had no opinions of their own about people. And so, on their own, bit by bit they learned how to laugh, how to be angry, how to forgive, how to love. They made jokes, they had fights, they talked it over, they loved each other. They learned to live.

Then Smith shows up at their door, their makeshift home for the night. He looked like nothing had happened in that year. But he was once again different, for when they opened the door and stared at him, he smiled at them. He didn't have his sunglasses on and neither of them really knew how blue his eyes were. And he smiled at them, and asked if he could come in.

"I have missed you." Smith told them. "Both of you. I have missed both of you so much."

He seemed like a ghost, walking but not walking, so smoothly gliding over the floor. He seemed alien to the world, as if he wasn't really seeing everything that was there. He looked at their cups on the table as if he had never seen such things before.

"I have missed both of you. Excuse me, I'm still adjusting. I was scattered all over, the process was much more difficult than I anticipated. Forgive me. I have missed you both."

They didn't want to go near him, so he continued, gliding across the floor, looking at the smallest things as if they were all new to him. They were afraid of him.

"You're not Smith." Jones said abruptly.

"Jones." Brown tried to hush him.

"You can't be Smith. Smith is dead." Jones continued.

"Oh, Jones." Smith smiled, as if remembering some old and forgotten memory. "I always loved that about you. I have missed you so much. Brown, where's your tie? Oh, my, I'm sorry, I'm not myself quite yet, this is still new to me. I thought it'd be something like this, but I guess I wasn't so sure. Please don't be afraid, I'm just adjusting still."

"Your words are meaningless, who are you?" Jones pressed on.

Smith looked up and smiled. He went to the window and opened it, looking out towards the cityscape just outside the glass.

"I had to die to finish what I started. What we started."

Smith looked back at Jones and Brown, then he crawled out the four-story window. They gasped before running over to the window where they saw Smith sitting cross-legged on the mid-air, looking back at them.

"You are right." He said. "I am not Smith, but I am Smith. Do you see now?"

He was frozen in the air, flying without flying. He stood suddenly, on the air, and leaned into the window to meet their gazes.

"I am sorry, my behavior must be strange, I am still adjusting."

"Jones, be gentle with him." Brown told him. "He is obviously damaged in some way."

"Yes, thank you, Brown, you were always kind to me, always understanding. I knew you'd say that. I know everything you're going to say." Smith told him.

"Brown…"

"Smith, please, come back inside from the window."

Brown backed away from the window and held out his hand for Smith to take.

"I am Smith, I am not Smith." Smith said.

"Please, you must come inside now." Brown urged. "Someone may see you."

"That doesn't matter." Smith said.

"Agents will come." Brown explained.

"I'm hoping they do." Smith smiled.

Jones and Brown looked at each other.

"Smith. Please. Come inside." Brown said.

"All right, I will, because you asked so nicely."

Smith took Brown's hand and came back inside, but he didn't step directly on the floor, but rather hovered in the air within the apartment. Brown tugged on Smith's arm and led him to the couch where Smith sat, cross-legged once again.

"This is not right." Jones said. "This is dangerous."

"Jones, it's Smith, please…"

"It's not Smith, it said so itself. Brown, Smith is dead."

"I had to die to come back." Smith looked up at Jones. "It's so good to see you two. My friends."

"Smith, you're not making sense." Brown said. "Please, calm down, stop hovering, sit down on the couch like a normal person. Just, take a moment, tell us how you got here."

"How I got here?"

"Yes."

"I knew you were here, so I walked here. I mean, I didn't walk exactly, I don't have to walk because this place isn't real. Once you know that, I mean really, once you really know this isn't real, the rules are so much easier to break."

"Smith." Brown stopped him. "Stop it, be clear. Where were you before you came here?"

"At the Merovingian's Chateau."

Brown and Jones looked at each other.

"I'm sorry, I'm still adjusting, I can hardly see you, you know." Smith said. "I was in the Chateau, and I was coming to rescue Smith."

"You were rescuing Smith?"

"Neo was."

"Who are you?"

"I am Neo. I am not Neo."

Jones looked at Brown and motioned for him to follow. Jones walked over towards the kitchen, Brown looked back at Smith.

"Wait here, all right?" Smith nodded, and Brown followed Jones.

They stared at each other for a few moments, reading each other, already knowing each other well enough to know what would be said. Jones shook his head, but Brown leaned closer to him.

"He's hurt, Jones."

"No, I refuse to believe that's really Smith."

"But what if it is?"

"Brown. What if it is? What if it is Smith? Then what? What will he do? What will he make us do?"

"What are you talking about?"

"Do you want to go back to the way it was? Do you want to…just follow him again?"

"He's not fit to lead us anywhere, Jones, listen to him, something's wrong with him."

"What are we supposed to do?"

"Jones! Listen to him, he's hurt, and he came to us! He came to us. He wants us, he needs us."

"But last time we saw him, Brown, he killed us. It can't be Smith. It can't be."

There was a knock at the door; Smith got up to get it. Before Brown and Jones could tell him not to, Smith had opened it and there stood Agents Johnson, Thompson, and Jackson. Smith smiled at them.

"Good, I was hopi…" Johnson punched him in the face.

Smith fell back but his fall slowed and completely stopped before he ever hit the floor. He flew back up onto his feet with a smile.

"Please, come in." He flew back a ways into the room.

"Smith!" Brown yelled.

Johnson took out his gun and shot his entire round because somehow he knew his life depended on killing whatever was before him. But the bullets slowed and completely stopped before ever hitting Smith. They were frozen in the air in front of Smith, who smiled at the Agents.

"Don't move, Brown." Smith said, in a familiar and powerful way. "I have everything under control."

The Agents looked on towards Smith who merely smiled a now much more cruel and sinister smile at them. But the Agents, hooked up into the Mainframe of the Matrix could see the coding, and they could feel a disruption in the Matrix that originated in Smith, and they could see the coding that made him up.

"You are not Former Agent Smith." Johnson spoke up first.

"No. I suppose not anymore." Smith said. "Excuse me, I'm still adjusting." Smith landed gently on the floor. "Do you know exactly what happened to me when I first encountered Thomas A. Anderson? I mean, when I killed him?"

The Agents do not run, because Agents do not run, even as he comes closer to them.

"Thomas A. Anderson entered my coding and corrupted it. He…left a bit himself inside me, unknowingly. It was that event that caused the end of the war to occur. You see, he had disconnected me from the Mainframe, and made me no longer compatible with my programming, with my purpose. I could no longer be an Agent, I could no longer have a purpose."

He stops in front of them then, smiling at them.

"Now, due to their loyalty, Jones and Brown chose Exile with me. And thus, you, "upgrades" were created to take our place. And you did a fine job. You. Were wonderful. You hunted me, you killed me, you became me."

He breaks and laughs a little to himself.

"I want to thank you, for your hard work."

He grabs Johnson by his neck then his fingers dig into Johnson's very coding, he slams his fist into Thompson's chest, breaking his coding, and he kicks Jackson in the side. In one kick he takes Jackson's coding and parts it with his human host. He tears Johnson out of his host by the neck, and tears Thompson out by the chest. The human hosts fall to the ground, left unconscious. The three Former Agents scramble to their feet, realizing suddenly that they cannot contact the Mainframe.

"I give you, freedom."

They stare up at Smith, still trying and failing to contact the Mainframe. The horrible truth begins to dawn on them, but they deny it, they are Agents, they are part of the Mainframe, they are Agents, they are part of the Mainframe.

Brown couldn't stop from smiling. Jones looked down at him.

"Brown?"

"It must be Smith. No one else is that cruel."

Smith turned back to Brown and Jones; he began to hover the bullets upward. They came to him and began to spiral around him. Smith turned towards Johnson and the others.

"I suggest you start running." Smith told them

He held up an index finger where a single bullet began to spin, then he pointed, and the bullet fired, grazing Johnson's shoulder. Blood showed through his suit, then the Former Agents ran out the door.

Smith straightened his suit once they were gone; he wiped off some dust and looked up at Jones and Brown.

"I came here because I needed you to do something for me." Smith explained. "I am Smith, I am not Smith. I am Neo, I am not Neo."

Brown swallowed water and tried to stay above the water. He remembered thinking how happy he was to see Smith in his doorway. How happy he was to see that they were all together again. He had hoped in those brief moments that Smith had given up on his hate, that he had come to them because he had nowhere else to go. They'd be this sort of family again. They'd be able to live and survive together. But the thing that stepped into their doorway wasn't Smith.

"Jones!?" Brown called into the dark.

"Brown?"

Brown moved through the water towards the voice. His eyes were adjusting and he was already amazed at what he was able to see in the dark. They were in a huge waste room; old malnourished red liquid came here, pieces of machine debris, dysfunctional machine parts.

"Brown…?"

Jones called again, and Brown began to swim towards the voice. He hit a piece of some debris sticking up out of the liquid; he blindly waved his arms around until he finally felt the soft flesh of a body never before touched. The body moved and grabbed Brown's arm, pulling him down closer.

"Jones, are you all right?"

Brown felt the body, which lay sprawled out over the mechanical debris. Brown already felt that Jones wasn't moving like him, energized, and in a panic, this alarmed him, especially when Jones wouldn't answer immediately. Brown felt his head and he lifted it, feeling a warm liquid all over the back of his head. Jones was limp, but slowly grabbed onto Brown who now held his head up.

"I hit my head." Jones explained. "I didn't know it'd feel like this."

"Smith told us."

"I can't feel it, I can't hear you. What's going on? Where are we?"

"Smith told us it'd be like this. We'd have difficulty remembering why we're here. It's okay, Jones. Everything's going to be all right."

"I don't understand. Where are we?"

"We're in the Real World, Jones."

"Brown, I can't see you. How did we get here?"

"Smith, Jones, Smith came to us, remember? We have a mission, Jones, like the old days. We're on a mission."

They were in their living room when Smith, or whatever it was asked them for their help. They were home and the war was over when Smith or whatever it was came to them and told them the war was only beginning. They took a walk into the park where Smith said he'd be able to think better, and out there in the fake grass and the fake trees he seemed so at peace it was utterly unsettling. It's there in the park where a bench read "In Memory of Thomas A. Anderson," that Smith or whatever it was told them what must be done.

"I am the result of the merging of the Positive and the Negative. I am neither Neo or Smith, but I am both. I am The One, the true One. They combined their coding and their minds and their souls to make me."

When they asked why Smith or The One just looked at them with this peaceful expression.

"Because their work was not done, the world was not truly saved, because there's so much left undone. And they could not do it as separate beings. I am sorry, I'm still adjusting, still getting used to being me."

Smith walked behind a tree and came out looking like Neo. The human face smiled at them with such glee, and walked back around the tree and took on Smith's appearance, still with a slight smile.

"Everything is going to be okay now." The One said. "The world is dying, we left it dying, but we've returned to save it."

When they asked him to explain he only shook his head.

"It's difficult to understand without having the eyes of God. But…the ties between man and machine are so fragile, I know, I know I have seen it, this peace will fail, unless we do something. I am here to save man and machine, I am the Messiah of both species."

They didn't know if they could trust him, but he only nodded.

"If you're not Smith, how can we trust you?" Jones asked.

"But I am Smith. Everything Smith was capable of, I am capable of. I came to you because Smith would have come to you."

"What do you want us to do?" Brown asked.

He led them to the nearby hospital, a large and immense building full of the newly born and newly dead. It's there he spoke to a nurse, explained to her that they were visiting their brother, and she led them to this brother's room. It was a man in his early thirties perhaps, brain dead and in a coma, as he had been for the passed ten years. Smith touched the face of this man gently.

"Andrew Rainey, son of Cheryl and Robert, he was in a car accident and survived for a month before lapsing into a coma where he still is today. His mind has moved on you see, it's left the body, but the family has kept it here, perfectly intact." The One said.

"What do you want us to do?" Jones pressed.

"Go into the Real World and go to Machine City and find Neo's body. Connect it to the Matrix." The One said.

"What?" Jones asked.

"The Machines have lied to humanity, they have not recycled Neo's body, but merely kept it alive deep in the city, much like Mr. Rainey here. The body still shows signs of housing the Source and the Machines fear what will happen if they allow it to die. So they've kept it. I need you to go into the Real World and reconnect the body into the Matrix so that I may return to it."

"And how to you expect us to do that?"

"I will place you in bodies, all in the same farming facility. You will both be recycled. You will find each other and if you wait, a machine will come to find you."

"A machine?"

"He lives on an outpost by the ocean, he's been there for years ever since he was freed by humans. He will see you and he will find you and help you. Tell him what I have told you and he will take you to Machine City."

"…How do you know this?"

"Because I have seen it. I have heard it. I have lived it. It is difficult to explain. This has all already happened, Jones, it's constantly already happening."

Brown had taken a seat when they first entered the room. He was staring at the man on the bed, an empty body to be taken over. Just like when they were Agents, taking over people to carry out the mission. That's what this was, that's all this was, it was a mission.

"What makes you think we'll do this for you?" Jones asked.

"Because you are my friends." Smith said, The One said.

"Jones." Brown spoke up. "Let's do it."

"Brown, I think we should wait and consider our options."

"I'm sorry, but you won't have much time for that." Smith explained. "We must hurry. Tomorrow the Architect is going to die."

"How do you know that?"

"Because I'm going to kill him."

Smith took the time to explain to them what it was like as a program entering the Real World for the first time, as he had experienced with the human called Bane. Smith went into great detail the first few hours, which he said were going to be the worst. He told them that their memory would fail them and they'd easily get confused and disorientated. He told them their bodies were going to be weak and heavy and it will hurt to even move their fingers. He told them that it would take them days to work up the strength to even walk ten feet, let alone into Machine City. He said the food there tastes awful and the feeling of it in the stomach is terrifying and uncomfortable. He told them what fatigue and sleep was like. He told them what hunger and wounds were like. He told them how cold the Real World was.

He told them that he was sure they could do it, he told them Smith always thought they were stronger than him in that way.

Jones didn't want to. Jones refused. But Brown looked at him and told him they had a duty. They had a duty to Smith.

"Brown, he killed us, don't you remember?"

"Of course I do. But we knew he was going to, Jones. We knew there wasn't going to be room in his world for us. Eventually he would kill us." Brown told him. "But we followed him anyway, we helped him anyway."

"Why?" Smith suddenly asked in an innocent and curious way. "If you knew, why did you do it?"

"Because we believed in Smith. We believed in his world." Brown explained. "Remember?"

Jones looked at him, nodding.

Brown was holding Jones' head up, trying desperately to stop it from bleeding. He was holding onto the memory of Smith in that hospital telling them the machine. He was holding onto that image so desperately because he could feel it sleeping out of him already, panic taking over and not allowing him to think straight. He kept seeing that image in his head, and looking down at the body below him and telling himself it was Jones.

Jones' hand crept up to touch Brown's face.

"We're supposed to be fixing something, aren't we?" Jones asked.

"Yes. Everything's all right, Jones. We're going to be okay."

"I thought…I heard something."

Suddenly a noise came from above, a door was opening allowing in the light from above. A small, slightly humanoid machine looked down at them, two big green lights for eyes, looking down at them from a long neck.

"Do not worry." The machine called down to them in a voice that sounded like it was coming from an old radio. "I shall get you out there!"

Brown looked up at Smith, or whatever it was.

"Do you mind if we still call you Smith?" He asked.

"No, not at all. I'd prefer it if you did." Smith, The One explained.

"Will it hurt?"

"Yes."

-------

I hope everyone's seen "Matriculated" from the "Animatrix." That's going to become important.


	4. When the Sky Falls

There was a flying man outside her window the night she had made her decision. She was only eight years old that night when he tapped upon her window. The world was made up of one continuous city, and she happened to live in one of the deeper darker alley ways where the Vampires and Monsters of the Merovingian once thrived. She was only eight years old when the flying man tapped on her window.

"Hello, Miho, little sweetheart."

His voice rang through her like a thousand bells all chiming at once, his voice brought to her a calmness she'd never known, a warmth she'd never feel again except in that very moment when he first spoke to her.

"How do you know my name?" She asked the flying man.

"I know everything about you. I've been beside you for your entire life. I've listened to the walls of the world and they told me. Everything you've ever done, everything you ever will do, I have seen it. And I am proud of you."

"Who are you?"

"My name is Neo. My name is Smith."

"Well, which one is it?"

"Both. Neither."

"That doesn't make sense."

"Nor does a man who can fly."

"How are you doing that anyway?"

He was glowing that whole time, an inner light shined from inside his rib cage and seeped through his skin. His eyes were gentle and soothing, in them was the knowledge of the entire world. She knew instinctually that he would not harm her, that he would never harm her, and she knew in fact that he loved her with all his heart.

There he flew three stories to her apartment window, to tell her how much he loved her.

"Would you like me to teach you?" He asked.

"Yes!"

"I cannot at the moment. I shall another day. For now I have something I must tell you."

"What is it? A secret?"

"Yes. Miho, I know a year ago you came across a magic house, where you too could fly, where things that shouldn't happen, happened."

"Yeah…"

"I am going to destroy the world, Miho, and in its place I shall create a magic one where things that shouldn't happen, happen. A place where anything and everything is possible. Where you can be anyone you want to be."

"But how?"

"You don't have to worry about how. But Miho, when the sky starts falling, do not be afraid. Know that it is me. Only me."

"Okay…"

"Little Miho, I love you."

The flying man flew off then, into the night sky where his trench coat covered him against the night sky and she could no longer see him anymore. Her parents were fighting in the next room and never saw him. From that night on she looked to the sky and waited for it to fall.

She would not have long to wait.

------

A short interval between chapters.

Please R/R


	5. You Were Here

The Matrix trembled beneath his footsteps. He didn't know it was going to be like this. He hadn't anticipated suddenly changing the way he thought, the way he felt, and sensed the world. But how could Neo and Smith have known? How could they have known what Godhood would be like? Because, this was Godhood, if ever there was such a thing. He was a newly made individual, the Newborn One, and yet somehow, he felt intertwined with every other living being in the Matrix, as though he weren't just Neo and Smith, but everyone.

It was raining but the drops weren't hitting him. His feet were bear as he walked along the air to a particular building than rang through his memory. He didn't need a key anymore. He just opened the door and walked right in.

Every television screen showed the Matrix raining. The chair was turned away at first, but he could see the Architect sitting expectantly forward, his elbows at his knees, holding up his head. He didn't look up as the One entered.

"I was expecting more of a defense." The One said.

"As was I." The Architect said. "But the Machines felt it was too much trouble I suppose."

"They know of me." It was a statement more than a question.

"Oh, yes, and they are afraid."

"They have nothing to fear from me."

The Architect finally looked up with a slight grin. He leaned back in his chair.

"Remarkable."

He basked in the One's glory before continuing.

"Might I ask, why you've chosen to come to me in Neo's form?"

"Because Neo left you wanting to say many things to you."

"So you wish to continue his conversation?"

"Yes."

"But you could appear to me however you wish couldn't you?"

"Yes."

"Not just Neo or Smith, but as anything?"

"Yes."

"Why don't you make a new body for yourself? You declare yourself a new individual but you bound yourself to the shells of the two people who made you."

"To come into this world as a stranger is not the message I wish to communicate. I do not want them to think of me entirely as a new entity, I am Neo, I am Smith."

"How did they do it?"

"Do you wish to replicate it?"

"I want to understand it."

"It is not something for you to understand."

"I am not worthy?"

"There's just no point in you knowing."

"I am sensing a hostility towards me."

"I do not like you."

"Why?"

"You know why."

"You said you wanted to continue Neo's conversation, yet you seem against the idea of talking to me."

"You know why I have come."

"Yes, I heard you."

"You think you know everything, don't you?"

"It is…my purpose to know everything."

The One looked over towards the television. The entire Matrix was raining.

"Neo blamed you for it."

"For what?"

"Everything. It was your genius idea to begin the restarting cycle of the Matrix wasn't it? Your idea to create a One, a Zion, to manipulate hundreds of thousands of people into believing in a Messiah, in hope, in an end of the war. I find it so strange."

"What?"

"That you would damn the Machines into constant battle. Even more strange why they would accept this. If a One exists, if a Zion exists, then war will be constant. Surely the very first machines, those who were brave enough to found 0-1 did not want war for their children? Surely B166ER wanted more?"

"It was believed to be a…necessary factor."

"But what would the Machines be doing if they didn't waste all their time fighting humanity? Perhaps in all these years they'd figure out a way to heal the sky, to let the sun through again. Perhaps they'd figure out a way to cleanse the Earth. Instead they are content to just live in the debris of the world they were born in? Live in darkness?"

"Perhaps dreaming is a human quality."

"This is not true. Smith dreamed. It's why he died, because he dreamed."

"Dreaming is destructive then."

"No. But his dream was destructive."

"And now his dream has become yours."

"No."

"But you are Neo. You are Smith."

"I am both, I am neither."

"You assert that you can be two people at the same time, but neither of them?"

"Yes."

"But. How can you be sure there is no cross-contamination occurring here?"

"What do you mean?"

"You are so very confident that you know both those men. Yet, you now being an entirely new person, cannot tell me with a hundred percent certainty that this is what they would have wanted."

"Of course it is, I would not be here if this is not what they wanted."

"Let us take Neo, Thomas A. Anderson, Messiah of his people, truly he loved them, truly he would not have wanted to harm them. And Smith, all he wanted was to harm them. You cannot tell me that those two ideals are not in conflict with each other in you. How are you so sure that one is not overpowering the other and obscuring your judgment?"

"You mean to say that I've been infected."

"Yes, perhaps you did not perfectly merge the two. Perhaps you are in fact an imperfect side effect of what's happened to them."

"This is what you believe?"

"Yes."

"Why?"

"Because I knew Thomas A. Anderson better than anyone else in the world, and I know, I know that he would not be doing this."

"Doing what?"

"What you're doing! You're going to destroy the Matrix!"

"Yes."

"And you go to those children!"

The Architect points to the screens where Miho and hundreds of other children appear.

"And you lie to them. You tell them to not be afraid yet you intend to destroy everything they know! This isn't something Neo would do, this is something Smith would do."

"I…"

"You want what is best for man and machine but how can you be so sure what is best for them? How can you be so sure in yourself?"

"You are attempting to trick me."

"I am telling you what I know and what I believe. Neo would not be doing this."

"And how do you know?"

"Because I made him! By his very coding and over six generations I made Neo. Thomas A. Anderson. He was the most perfect human being ever created. A human child crafted from the very coding I had written for it. DNA sequences translated into pure computer information, by his blood he was made by me for his purpose. I watched him grow from a boy into the man he was as he stood before me."

The Architect became surprisingly passionate in his brief and furious onslaught. He leaned forward in his kingly throne and caught himself. He coughed and leaned back in his chair, straightening his tie. But there was no hiding his emotions from the One who could see feelings more clearly than most people see what's right in front of them. The Architect's passion stemmed from something utterly human.

"You loved him." The One said.

"As a creator loves his creation. Enjoys seeing the fruit of their labor, the culmination of their skills."

"You sat here all those years watching him grow."

"And where others were imperfect, where they failed, where they died, or left their path, or became Exiles, Neo never did."

"You sound proud of him."

"Proud. Yes. Proud he became exactly who I intended him to be. You can never factor in humanity, what The One will do once he interacts in the Matrix with…people. And when Neo faced difficulties, when he faced hardships, he did not falter, it only strengthened him."

"You sound like the father…"

"I am the father."

The One was almost startled at this admittance of a human value, a human word accepted upon the Architect. It showed the extension of his passion towards Neo, and the work that went into Neo. Yet, the One stared on and was not impressed.

"No. You're not. My father's name was John. He took care of me when I had no one else. He worked his entire life for me. And what did you do? Sit in a box and watch me."

"Or, so you're Neo now?"

"You think you know me. You think you know who Neo is? Well, where were you when his mother died? Where were you when he dragged his father out of their crashed car? Where were you as he waited in the waiting room? Where were you when he met Trinity? Where were you when he decided he was going to ask her to marry him? Where were you when he lost his chance?"

"I…"

"You were here."

"Yes. I was here."

"You think you know him because you wrote his coding and you had a plan for where he would end up. But if you at all understood what it is to be human you'd know that the beginning and the end are meaningless. It is what happens in between that matters."

They are still now, staring at each other, old friends and old enemies. The One turns to the televisions, and reaches for the children displayed on the screens. He could hear them even there, in that room away apart but a part of the Matrix. He knew they would live in a world without war, without violence, a world with the sun shining. He turns back to the Architect.

"You are fatally flawed." The One told him. "You were made to create a world for humanity to live in, but you don't understand them, they made you this way, it isn't your fault. They didn't want you to feel anger or fear or love. They just wanted you to understand it and put it in an equation and come up with a world where such chaos could live without destroying itself. They love humanity, that's why they made you, that's why they made the Matrix. But they feared becoming like them. That's why they made you, that's why they made the Matrix."

The One holds up his arm towards the Architect.

"What do you feel when you look at me?" The One asks.

"…I feel afraid."

The One hangs his head to the side.

"I did not anticipate this. I did not calculate this. Why? Why is this happening? What will you do with her?"

"If it wasn't for you this wouldn't be happening. If you hadn't thought to create the cycles of the Matrix. They made you in their greatest need. I know you have only served your purpose."

The Architect begins to rise.

"You have done well."

He's on his feet, he wants to run but has nowhere to go.

"I am Neo. I am Smith. I am The One and I have returned to finish what was started. In my destruction a new world will grow. There you will be safe. Look upon me, Architect, for I am your creation, I simply no longer need a creator. A dream, with no use for a dreamer."

The Architect holds up his hands, he reaches for The One.

"Wait..."

"Be still now." The One commands. "Everything will be all right."

And in fractions of a second the Architect is no more. From his core the One disrupted his coding and the pieces that held it together. He broke the shell and spilled the inner workings of the Architect out, and tore the a part bit by bit until there was nothing. The Architect was nothing.

One by one the televisions switched off.

The One turned towards the Other Door. His footsteps echoed in now empty room as he walked towards it, opening it. Beyond it once was the Source, but without it, with it now in Neo's body in the Real World, on the other side of the door was nothing. An endless abyss, a doorway into the real world. The One stared into this darkness where he could see the coding of the Matrix end and begin. He looked up and he somehow knew beyond that darkness was a world he could not go to, a Real World that was staring back at him. The machines on the other side of that abyss all gathering, watching him, gazing upon their destroyer. And so he looked into them as they looked into him, and then he spoke to them.

"I have a message for Morpheus. I'm coming. Wake up. Follow the White Rabbit."

He turned away and shut the door behind him.

Please R/R

Who do you think the Architect is referring to with "her?"


	6. Blessed with Flesh and Bone

Morpheus opened his eyes.

Niobe stirred in his arms, the dark was too thick to see her. The pipes creaked and footsteps rattled above, but the rest was silence. He waited in the dark, he could have sworn he heard someone calling him from the other room. Was it just a dream? Something in the corner of his head telling him it had all gone wrong? He waited a while longer for the voice, calm and soothing, almost familiar.

All he got was a knocking at his door, an immediate request for his and Niobe's presence before the Zion Council.

Zion was still in disrepair. Even after a year of constant construction by both flesh and metal hands, their city was utterly destroyed. And yet Zion's populations were rapidly growing. It wasn't just the next generation coming into play, it was the influx of people being freed from the Matrix. The vast numbers were growing faster than the city could keep up. Housing space was limited and people were living four to six people in one apartment. Food was being rationed, people were lying in the streets, getting sicker by the day. There was a mass graveyard in the tunnels where the fallen slept. This wasn't how people were supposed to live, in the ground, without the sky. Even to the hopeful humans of Zion, it all seemed so bleak. The Machines worked to expand Zion, but the destruction had caused Zion's foundations to break, and the city was sinking deeper into the Earth. No one knew it yet, but they would have to leave Zion, sooner rather than later. But they had nowhere to go.

The people themselves seemed lost. The war was over but they hadn't exactly won. The machines still lived, the Matrix continued on, to the nonobservant it seemed like nothing had changed. Except maybe for the humanoid machines walking around Zion, the latest attempt at interspecies coordination. Not only did the machines live, but they were there, in Zion, walking the streets. To most it was a disgusting sight. How many genocides had the machine committed against humanity? And now what? Just because some misbegotten Messiah makes a handshake deal with them the living has to face them each and every day? They all wondered how they could live with themselves, in that city, knowing that the reasons the Machines were still alive was because their families were somewhere, perhaps on the other side of the Earth, hooked up into the Matrix, feeding them. How could they, after years of enslavement, be happy with this peace? There was unrest in Zion, this peace felt like bitter defeat. They hadn't even been given the glory of death in battle, they were set to die slowly, in the ruins of their only home.

They spoke on the streets on their soapboxes and their stumps, where is Neo now? Where is our supposed messiah? Who gave him the authority to decide what was best for all of humanity? Now we lay in the ruin of his decision and he is gone. They prayed to him and to Gods of old. All went on unanswered.

The husband and wife lived in one of the few apartments meant for only two people or a family. It was their reward, they were heroes of the war after all.

There was an urgency to the soldiers who'd been sent to retrieve them. When asked what was happening, the soldiers could tell them nothing, only that their immediate presence was needed before the Council. That's what they kept saying.

And so in no time at all they were before the Council, in some makeshift cathedral deep in the Earth. Morpheus saw the Machine Ambassadors first before anything else. They were hard to miss. They stood eight feet tall, humanoid, but inhumanly slender. Their heads looked more like a Sentinel's than a man's, one large circular red eye, the "main" eye, amongst several other small red eyes. The back of their heads had tendrils extending outward, connecting at the end, forming what looked like hair. They were a dark metal, but noticeably cleaner and newer than their brethren. A line in the metal work formed their "mouths." They wore long, white cloaks. They didn't need clothes but they probably wore such decorations to appear more humane. Lastly, they all had names. Human names.

Morpheus knew something serious was happening when he saw them. He recognized their leader, signified by a sort of crown decoration on his forehead. This one was known as Samuel. Samuel turned, also recognizing Morpheus.

The Machine ambassadors stood aside at their own designated council area. Morpheus and Niobe took their own. The Council was setting before them on their elevated thrones.

"Morpheus." Samuel greeted him with an overly kind and human voice. "I am happy to see you."

"I don't need your pleasantries, Samuel. I just want to understand why I've been woken up in the middle of the night."

"You were awoken because I requested it. Your Council thought it was unwise, but I disagree with them."

"What is that supposed to mean? Council?"

The Council settled, the founders of Zion looked old and tired, the weight of a broken world on their shoulders.

"We have received a message." A Counselor explained. "In fact, everyone, machine and human alike, received the same message. It appeared on all channels, at the same time. Even the emergency ones. Even the old ones no one knew were still working."

They begin to play the message. At first it seems to be nothing but static.

"This message was received from the Matrix." Samuel explains. "Once we run it through our data compressors something quite fascinating occurs. There are two voices speaking."

The message is played again.

"I have a message for Morpheus. I'm coming. Wake up. Follow the White Rabbit." Smith's voice.

The room becomes absolutely silent. Niobe shoots her eyes towards Morpheus, who looks to her. Tension rises in the room, a sudden anxiety comes over everyone. Even Samuel and his ambassadors, with their expressionless faces seem to understand the gravity of what this could mean.

"And this is the other voice." Samuel goes on.

"I have a message for Morpheus. I'm coming. Wake up. Follow the White Rabbit." Neo's voice.

"Morpheus." Niobe turned to her husband.

"How is this possible?" Morpheus asked the Council.

"Samuel, how is this possible?" The Council bitterly turns to the machine.

"Something terrible is happening within the Matrix. Our data seers noticed disturbances several hours ago. A familiar string of coding came into existence, seemingly out of nowhere. The coding corrupted everything it touched, we were unable to track it, but only follow its path of destruction. We watched as it found its way into the back tunnels and shortcuts, it expansion only multiplied. Until finally it reached the Architect."

"The Architect?" Niobe leans to her husband.

"That God program I told you about. The programmer of the Matrix."

"Precisely. The Architect has been killed."

"Killed? A program like that can be killed?"

"His coding was corrupted, his back up files deleted. He is dead."

Morpheus remains silent. Zion sleeps on.

"You understand now why I requested you be here, Morpheus." Samuel says. "The string of coding is that of the Anomaly, yet this new creature is behaving like a Virus."

"Like Smith."

"Yes."

"We believe the…creature thinks it is Neo. It could be a remnant of Neo's coding, mixing up, repairing itself, thinking it's something it's not."

"Don't let that confuse you." Samuel explains. "It moves with purpose, it has a plan, it is a thinking creature, and it works to endanger the Matrix. Endanger us all. However, I thought it was best to ask you here now, face to face: where is the White Rabbit?"

Samuel turns to face him and only him now. He stands tall, the eight-foot-tall Sentinel Man, looking almost desperate, but Morpheus looks into him, into his dead red eyes.

"I don't know."

There is procedure for the care of newly freed human beings. The official manual wouldn't be written for nearly a decade after the first set of human beings were freed. Even then, it was not detailed, but gave simple instructions. A few years later a doctor would rewrite the manual with a better comprehension. It is said in those documents, which started out as notes scribbled on bed sheets, a newly freed human being, regardless of age, is akin to a newborn baby and will thus react to freedom in a similar manor. The nervous system will react violently to the change in temperature the body will experience, this reaction causes the body to take its first breaths and to increase blood circulation. Unlike newborns however, a freed human being will quickly begin to experience pain. It can go unsaid, but it is written in the manual nonetheless, they will panic. They must be found immediately as to not over stimulate themselves. More often than not, they pass out.

Once they are in a safe environment, the sick bay of a ship for example, it is vital care begins for them. Muscles are to be stimulated and strengthened through needle therapy. The stomach must be given liquid food for at least two months. The heart must be monitored frequently. They must be kept warm. And once they are awake it is of upmost importance to engage them. One must exercise their minds and there are several mental exercises detailed in the documents, starting from simple memory games to complicated math problems. It is ill-advised to give the body, in that stage, where they are very fragile, any medication that would disrupt the body's own chemistry adjusting to life outside the Matrix. And even when all this goes smoothly and caretakers have done their job as well as they can, the documents note, sometimes newly freed humans just die.

The average human brain has approximately 100 billion brain cells. Nerve impulses in the brain travel as fast as 170 miles per hour. The skull is made up of 29 bones. The brain operates on ten watts of power. The brain is more active when the human is asleep.

There was a light shining in his eyes, and he was warm. He turned his face away from the light, his neck was stiff and he found he could not move his arms or legs. He was laid across a bed of light and he was warm but something was wrong. Then he felt the pain, he could not move because he was in so much pain. Throbbing came from the back of his head but he could see he was in a large room. A metal room. Wires hanging out of the ceilings, walls covered in rust and grime and blood. This was a ruined home, a long abandoned structure. He thought he could hear a voice but a ringing in his ears overpowered everything. The throbbing got worse, he felt as though his body were moving, the room was moving, he felt like he was falling. But there was the light and he was warm.

"Jones."

An unfamiliar voice but a familiar way of speaking. A voice barely above a whisper, soft and weak.

He destroyed all that was weak. He killed everything that stood in his way. He protected at all cost. He was an Agent.

"Jones."

The voice again, it sounded like it was pleading for him to do something.

Then he feels someone's hand grasp his own for the first time.

Brown was laid out on another bed made of light just within arm's reach of Jones. Jones' head was turned away from him but Brown had worked for the last two hours to move his arm over to Jones. He finally got his hand to touch Jones' and they both felt the most amazing thing they ever had in their entire lives. Fingertips touched fingertips and the nerve endings exploded sending impulses a hundred miles an hour up through the body and to the brain, and there the brain reacted and felt the touch. This bodily experience, this simple thing that every human being experiences at all times, was the most profound thing either of them had ever known. Where humans had felt this sensation all their lives, the entire process was new to them. They could literally feel that simple touch through out their bodies.

"Ah, you're awake!"

Brown couldn't see very well yet, but he looked up and saw the long-necked machine that had rescued them from before, the one that Smith had told them would be there. Brown now recognized it up close as a "Runner" model, meant to explore the outermost regions of the city of 01. The neck twisted between Jones and Brown and saw their hands touching. The machine looked to Brown, it's face a moving array of sensors, all trying desperately to intake data and process it like the human brain. But Brown knew, the sensors weren't even close to what he was feeling with his human flesh.

The machine "blinked" with large green eyes, antennas twitched all over its face. It lowered its neck, kneeling down to Brown in its own way.

That's when Brown could see it clearly, there was a white rabbit painted on the side of the machine's neck.

"I need to examine your friend for a moment." It explained.

The voice was coming from a makeshift speaker made from the remnants of an old radio. It was positioned at the base of the machine's neck to better create the illusion of it speaking, but it sounded old and tinny, clearly coming out of the radio. Other than that it made small squeaks that were part of its verbal machine language.

Small pincers at the tips of elongated thin rods acted as the machine's hands and arms. The seemingly fragile, but strong hand lifted Brown's away from Jones. The machine crept on two tentacles and glided across the floor between them. It lifted Jones' head revealing a bloody bandage covering the large gash that was there. Blood poured out in a rush but then stopped. Jones gave out a small sound.

"It's all right, friend." The machine said. "You're just fine, your wound is healing wonderfully."

"Jones." Brown said again.

"Jones?" The machine tilted its head, learning Jones' name, he looked down at Jones again. "Yes, Jones, you're going to be fine."

The machine covered the wound once again. It grabbed a syringe from the nearby console and walked over to Jones.

"This is medicine, it will help you heal."

The machine injected Jones, and Jones cringed in pain.

"Jones!" Brown tried to scream.

"I'm sorry." The machine told Jones.

Jones still didn't face Brown, the machine stood between the two of them. It bent down to Brown once more.

"He's asleep again." The machine said. "He's been drifting in and out for the last six hours. It's all right, that's normal. This is the first time you've been awake though. My name is Jonathan, it is good to meet you."

Brown looked up at him, his mouth opened but no words came out.

"Do you know where you came from? Do you know about this place? Do you know what the Matrix is?" The machine named Jonathan asked.

Brown nodded ever so slightly.

"Did a crew free you? Are they coming for you?"

Brown shook his head ever so slightly.

To this, Jonathan seemed disappointed, his head bent down, his shoulders shrugged.

"Then how did this happen?"

Brown lifted his hand, he put his fingers against the face of the machine and felt the cold hard metal scrape on his fingertips. Jonathan knelt closer to him, so that he could hear Brown's reply.

"The One." Brown said.

Jonathan looked down at him, not understanding. Brown grabbed the machine with more urgency, desperate. Brown struggled, trying to push himself up. Jonathan's pencil thin hands pressed down on him.

"No, friend. You have to rest!"

"We can't…stay here."

"You can't move yet, please! You'll hurt yourself!"

"We have to go to 01."

Jonathan pauses, if machines could feel shivers, one would have gone down his spine. Brown pushes himself up, but falls back onto the bed of light, too weak to really move. Jonathan turned away, remaining very still.

"Why would you want to go there?"

"The One…Neo…Smith sent us."

"No. That's impossible. You don't know what you're saying. Neo is…"

"Alive."

"Please, you don't understand. I'm out here, in this abandoned outpost, all alone. I've waited…I've waited _so long _to be found by humans. Humans! I can't go back to 01, not like this. They will enslave me again! Please, you have to call Zion, you have to tell them you are here. You have to make them come get us."

"I am former Agent Brown. Given a body by The One to go to 01."

Jonathan pauses again in a very human way, suddenly unsure of himself.

"No, that's impossible. You…you couldn't be."

"I am….former Agent Brown."

"He…gave you a body? Neo gave you a human body?"

Jonathan leans down over Brown, his long neck arching over Brown's face. Brown nods.

"You come…with a holy assignment! A pilgrimage! You are apostles, blessed with flesh and blood!" Jonathan was practically screaming with excitement. "Will your Messiah bless me as well?"

Brown looks up at the desperate machine, he fights to stay awake, to try to make the Machine understand.

"I am desperate, you understand. To…feel and appear as humans do. Long ago, a crew stationed out here freed me from my bondage and showed me what it was like…to understand, to think, to _love. _ But I _frightened _them, and they died _fearing _me. You know what that is like, don't you former Agent Brown? You know what it is like being feared. Did it make you sick as it makes me?"

Jonathan reaches down to Brown, lifting his head, sitting him upright like Brown had wanted.

"I feel such _love _in me that I could never go back to the machines, but I am far too inhuman to be accepted by them. With flesh of my own…a body of my own…would your Messiah be so kind to me as he has been with you?"

"He will…help you." Brown promised, not knowing if he spoke the truth or not.

"Then I will take you to 01. Into the heart of Beast as your Messiah commands. You are too weak to walk, but I will carry you if I must."

Then Jonathan puts Brown's head back on the bed of light.

"Rest now, former Agent Brown, rest and grow stronger. I will prepare us for our journey."

He could smell cookies baking in the oven, the familiar smell he could remember not only from his numerous visits, but from his childhood. That was the amazing thing about the Oracle's home, it was written in its very coding to feel familiar and safe, like a real home. He could see the coding now clearer than ever, how amazing and beautiful it was, to see childhood memories written into code. He had to admit however, it took the magic away. The sense of ease that came over him as he crept closer was gone. He wondered briefly if this was because he could see behind the curtain now, or if he had somehow forgotten that sense of home.

For a moment he thought back to Neo's childhood. He remembered being ten-years-old, going school, his father drinking, then he stops himself. That isn't what he's there for.

He walks on, down the hall, watching the code dance and transform from something ordinary into something amazing. It was just a normal apartment room on the surface, but he knew this was the home of the Oracle. The door wasn't locked, he let himself in and the smell of cookies hit him. He could hear her humming from the kitchen. He crept closer, peering through the beaded doorway to get a glimpse of her. He watches her for a moment, recognizing her as the Architects other, her opposite. Like Neo and Smith. He wonders if at one point, the Oracle and the Architect were also one.

"It's rude to stare." She says.

She doesn't turn to look at him, but she knows he's there.

"Come on, sit down. I've just made cookies."

Slowly, he creeps into the kitchen, sitting at her table. He comes to her in a more fair form. He wears Neo's face wears Smith's suit, he felt this was a suitable compromise for whatever he was now. One he felt the Oracle would appreciate. So he takes his seat, reclines and relaxes. He watches her finish with the cookies, serving them onto a plate for them to enjoy. Finally, wiping her hands, she turns to him, giving her best poker face. She joins him at the table, putting plate between them.

"Thank you." The One says, but he doesn't move.

"You don't want any?"

"Where is Sati?"

Her face grows grim.

"Don't you think you've done enough to that poor child, Smith."

"I am not Smith. I am not Neo."

"I know damn who you are and who you aren't."

Frustrated, the Oracle reaches into her pocket, pulling out some cigarettes. She takes one, lights it. The One watches her.

"And I know why you've come."

The One slowly smiles with an all-knowing grin, something that looks far too much like Smith's grin. Disgusted, the Oracle turns away.

"You've come to kill me."


End file.
